Proteins: Levels of Protein Structure Conformation of Peptide Group CHMI 2227E Biochemistry I Proteins: Levels of Protein Structure Conformation of Peptide Group CHMI 2227 - E.R. Gauthier, Ph.D.

Proteins: Levels of Protein Structure Individual proteins molecules can be described by up to four levels of structures Primary Structure Secondary Structure Tertiary Structure Quaternary Structure http://macromolecules.ucsf.edu/Lectures/Tanja%20Macromol_forces%202006.pdf CHMI 2227 - E.R. Gauthier, Ph.D.

Primary Structure Sequence of amino acids in the polypeptide chain; Primary structure is a complete description of all the covalent bonding in a polypeptide chain or protein; In some proteins, the linear polypeptide chain is cross-linked Disulfide bonds However, the primary structure does not indicate the position of the amino acids in space http://www.fiu.edu/~bch3033/Handouts/Lh4Ch04Prot.pdf CHMI 2227 - E.R. Gauthier, Ph.D.

Secondary Structure It is the ordered arrangement or conformation of amino acids in localized regions of a polypeptide or protein molecule; Hydrogen bonding plays an important role in stabilizing these folding patterns; The two main secondary structures are the alpha helix and beta-pleated sheet http://www.fiu.edu/~bch3033/Handouts/Lh4Ch04Prot.pdf CHMI 2227 - E.R. Gauthier, Ph.D.

Tertiary Structure It is the combination of all of the secondary structures adopted by the different local regions of the protein; It is the 3D arrangement of the atoms within a single polypeptide chain; http://www.fiu.edu/~bch3033/Handouts/Lh4Ch04Prot.pdf CHMI 2227 - E.R. Gauthier, Ph.D.

Quaternary Structure It is used to describe proteins composed of multiple subunits (multiple polypeptide molecules each called a monomer); The subunits can be identical or different; Most proteins with a molecular weight greater than 50 000 Da consist of two or more noncovalently-linked monomers; The arrangement of the monomers in the 3D protein is the quaternary structure http://www.fiu.edu/~bch3033/Handouts/Lh4Ch04Prot.pdf CHMI 2227 - E.R. Gauthier, Ph.D.

Proteins The formation of higher levels of organization (2°, 3° and 4°) is done is a very precise way; A protein usually adopts a single tertiary structure: this is also called the native conformation of the protein For proper folding, weak non-covalent forces are required CHMI 2227 - E.R. Gauthier, Ph.D.

CHMI 2227 - E.R. Gauthier, Ph.D.

Secondary Structure of Proteins The elucidation of the secondary structures of proteins was possible only after understanding the geometry of the peptide bond http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olunderstandconfo.html The peptide bond is essentially planar CHMI 2227 - E.R. Gauthier, Ph.D.

Conformation of the Peptide Group If the peptide bond is planar, therefore, the two atoms involved in the peptide bond along with the four substituents (carbonyl oxygen atom, the amide hydrogen atom, and the two adjacent α-carbon atoms) lie in the same plane Peptide Group CHMI 2227 - E.R. Gauthier, Ph.D.

Peptide bond has resonance structures! Peptide bond is shown as single C-N bond Peptide bond is shown as a double bond Actual structure is best represented as a hybrid of the 2 resonance structures in which electrons are delocalized over the carbonyl oxygen, the carbonyl carbon and the amide nitrogen. Rotation around the C-N bond is restricted due to the double bond nature of the resonance hybrid form Note: Peptide bond is polar! The oxygen and nitrogen atoms have partial negative and positive charges, respectively CHMI 2227 - E.R. Gauthier, Ph.D.

Conformation of the peptide group Peptide bond has a double bond nature, therefore, the conformation of the peptide group is restricted to one of two possible conformations, either Trans or Cis CHMI 2227 - E.R. Gauthier, Ph.D. Figure 3.25 Biochemistry 2001, Fifth Edition

Cis conformation of the peptide group The two α-carbons atoms are on the same side of the peptide bond and are closer together; The cis conformation is less favorable than the extended trans conformation because of steric interference between the side chains O H C N Cα Cα R1 R2 CHMI 2227 - E.R. Gauthier, Ph.D.

Trans conformation of the peptide group The two α-carbons atoms are on opposite sides of the peptide bond and at opposite corners of the rectangle formed by the planar peptide group; Consequently, nearly all peptide groups in proteins are in the trans conformation R1 H C Cα Cα N O R2 CHMI 2227 - E.R. Gauthier, Ph.D.

Exceptions to the rule! Cis conformation does exist; Figure 3.26 Biochemistry 2001, Fifth Edition Cis conformation does exist; Most common is the X-Pro linkage 10% of the proline residues in protein follow a cis peptide bond These bonds show less preference for the trans conformation because the nitrogen of proline is bonded to two tetrahedral carbon atoms limiting the steric differences between trans and cis forms CHMI 2227 - E.R. Gauthier, Ph.D.

Psi and Phi Angles In contrast to the peptide bond, the bonds between the amino group and the α-carbon atom and between the α-carbon atom and the carbonyl group are pure single bonds The rotation around N-Cα bond of the peptide group is designated Φ (phi) and that around Cα-C is designated Ψ (psi) CHMI 2227 - E.R. Gauthier, Ph.D.

Psi and Phi Angles Each of these angles is defined by the relative position of four atoms of the backbone; Clockwise angles are positive and counterclockwise angles are negative with each having a 180° sweep; Each rotation angles range from -180° to +180° Peptide Bond CHMI 2227 - E.R. Gauthier, Ph.D.

Psi and Phi Angles The two adjacent rigid peptide units may rotate about these bonds taking on various orientations; These rotations are restricted by steric interference limiting the permissible angles Interference between main-chain and side-chain atoms of adjacent residues Interference between carbonyl oxygens on adjacent residues CHMI 2227 - E.R. Gauthier, Ph.D.

Animation of Phi rotation http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olunderstandconfo.html CHMI 2227 - E.R. Gauthier, Ph.D.

Animation of Psi rotation http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olunderstandconfo.html CHMI 2227 - E.R. Gauthier, Ph.D.

Ramachandran Plot Biophysicist G. N. Ramachandran constructed a space filling model of peptides and made calculations to determine which values of Φ and Ψ are sterically permitted in a polypeptide chain Permissible angles are shown as colored regions in the Ramachandran plots of Φ vs Ψ CHMI 2227 - E.R. Gauthier, Ph.D.

Ramachandran Plot The conformations of several types of ideal secondary structures fall within the shaded areas Blank areas are nonpermissible angles due to steric hindrance CHMI 2227 - E.R. Gauthier, Ph.D. Figure 3.28 Biochemistry 2001, Fifth Edition